Hello,
I have installed miso using root. Now i am trying to execute command and got error every time...
miso --run ~/miso_annotations_hg19_v2/indexed_SE_events/ ~/Sample.sort.bam --output-dir OUT/ --read-len 49 --paired-end=147 27 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
Error==Waiting on 4 threads...
Then I increased number of threads but still ended in errors.
After that I started job in cluster mode using following command but still I got following error.
miso --run ~/miso_annotations_hg19_v2/indexed_SE_events/ ~/Sample.sort.bam --output-dir OUT/ --read-len 49 --paired-end=147 27 --use-cluster --chunk-jobs 50 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
WARNING - Asked to wait on cluster jobs but cannot parse their job IDs from the cluster submission system.
Any suggestion is appreciated. I saw few related posts on similar issue and tried almost everything but still getting error.
Thanks in advance.
I met the same questions as yours. Have you solved it? Could you tell how to do this? Thank you!
When you get this issue try to run following command stead.
python ~misopy/run_miso.py --compute-genes-from-file "~batch-genes/batch-0_genes.txt" ~/Sample.sort.bam ~OUT/ --read-len 49 --paired-end 147.0 27.0 --settings-filename miso_settings.txt